Rare Nonsynonymous Variants in Alpha-4 Nicotinic Acetylcholine Receptor Gene Protect Against Nicotine Dependence

Abstract

Background There are several studies reporting association of alpha-4 nicotinic acetylcholine receptors (encoded by CHRNA4) with nicotine dependence (ND). A meta-analysis of genomewide linkage studies for ND implicated a single chromosomal region, which includes CHRNA4, as genomewide significant. Methods After establishing that common variants are unlikely to completely account for this linkage, we investigated the distribution of CHRNA4 rare variants by sequencing the coding exons and flanking intronic regions of CHRNA4 in 209 European American (EA) ND cases and 183 EA controls. Because most of the rare variants that we detected (and all nonsynonymous changes) were in exon 5, we sequenced exon 5 in an additional 1000 ND cases and 1000 non-ND comparison subjects, both of which included equal numbers of EAs and African Americans (AAs). Results Comparison subjects had a higher frequency of rare nonsynonymous variants in the exon 5 region (encoding the large intercellular loop of the α4 subunit) (Fisher’s exact test p=0.009; association test p=0.009, OR=0.43; weighted-sum method p=0.014), indicating a protective effect against ND. Considering data from the two stages combined and only nonsynonymous variants predicted to alter protein function, the association was stronger (Fisher’s exact test p=0.005; association test p=0.008, OR=0.29). SPECT imaging results were consistent with functionality. Conclusions CHRNA4 functional rare variants may reduce ND risk. This is the first demonstration that rare functional variants at a candidate locus protect against substance dependence, suggesting a novel mechanism of substance dependence heritability that is potentially of general importance.

Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses

“…[24][25][26][27][28] These studies come to similar conclusions: that it is not a single variant acting alone that is causal, but rather sets of variants. 24,25,28 The sets they identified are rare variants that overlap with functional annotations such being missense or nonsynonymous variants.…”

“…[24][25][26][27][28] These studies come to similar conclusions: that it is not a single variant acting alone that is causal, but rather sets of variants. 24,25,28 The sets they identified are rare variants that overlap with functional annotations such being missense or nonsynonymous variants. Several of these previous studies focused only on exons, [24][25][26]29 and therefore would have missed 22 out of 27 (81.5%) of the single locus top findings and 23 out of 33 (69.6%) variant set top findings.…”

Rare Human Nicotinic Acetylcholine Receptor α4 Subunit (CHRNA4) Variants Affect Expression and Function of High-Affinity Nicotinic Acetylcholine Receptors

“…Rare variants in CHRNA4 also appear to be underrepresented among smokers (Xie et al, 2011). A particular rare variant (a4P451L) has also been associated with development of amyotrophic lateral sclerosis (ALS) (Sabatelli et al, 2009(Sabatelli et al, , 2012, suggesting that it may be of particular functional interest.…”

Translational Research in Nicotine Dependence

“…For example, SNPs in CHRNA6 and CHRNB3, the genes encoding the a6 and b3 subunits, have been associated with nicotine dependence, subjective response to nicotine, and self-reported number of unsuccessful quit attempts (Bierut et al 2007;Greenbaum et al 2006;Saccone et al 2007;Zeiger et al 2008;Hoft et al 2009). Additional studies have implicated the gene encoding for the a4 subunit, CHRNA4, in various smoking phenotypes (Breitling et al 2009;Wessel et al 2010;Han et al 2011;Xie et al 2011). Furthermore, polymorphisms in the CHRNA4 gene have been significantly associated with abstinence rates while on nicotine replacement therapy (Hutchison et al 2007) or varenicline (King et al 2012), suggesting a potential role for CHRNA4 as a target for therapeutic intervention.…”